Release Notes

Release 10.0, Tuesday April 26th 2005

Acknowledgements

R.Apweiler (1), T.K.Attwood (4), A.Bairoch (2), A.Bateman (5), D.Binns (1), P.Bork (8), P.Bucher (3), M.J.Campbell (14), L.Cerutti (3), R.Copley (13), E.Courcelle (6), U.Das (1), L.Daugherty (1), M.Dibley (7), R.Durbin (5), W.Fleischmann (1), J.Gough (11), D.Haft (9), N.Hulo (2), S.Hunter (1), D.Kahn (6), A.Kanapin (1), M.Krestyaninova (1), D.Lonsdale (1), R.Lopez (1), I.Letunic (8), M.Madera (12), J.Maslen (1), J.McDowall (1), J.Mistry (5), A.Mitchell (1,4), N.Mulder (1), A.N.Nikolskaya (10), S.Orchard (1), C.Orengo (7), M.Pagni (3), D.Peyruc (6), E.Quevillon (1), C.Sigrist (2), V.Silventoinen (1), P.D.Thomas (14), R.Vaughan (1), C.H.Wu (10).

(1) EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK;
(2) Swiss Institute for Bioinformatics, Geneva, Switzerland;
(3) Swiss Institute for Experimental Cancer Research, Lausanne, Switzerland;
(4) School of Biological Sciences, The University of Manchester, Manchester, UK;
(5) The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK;
(6) CNRS/INRA, Toulouse, France;
(7) Biochemistry and Molecular Biology Department, University College London, University of London, UK;
(8) Biocomputing Unit, EMBL-Heidelberg, Germany;
(9) The Institute for Genomic Research, Maryland, USA;
(10) Protein Information Resource, Georgetown University Medical Center, Washington, D.C., USA;
(11) Genomic Sciences Centre, RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Japan;
(12) MRC Laboratory of Molecular Biology, Cambridge, UK;
(13) Wellcome Trust Centre for Human Genetics, Oxford, UK;
(14) Computational Biology, Applied Biosystems, 850 Lincoln Center Drive, Foster City, CA 94404, USA.

Current Release

Introduction

The databases UniProt, PROSITE, PRINTS, Pfam, and ProDom joined forces to launch an Integrated Documentation Resource of Protein Families, Domains and Functional Sites, abbreviated InterPro. Since then SMART, TIGRFAMs, PIRSF, SUPERFAMILY, and more recently PANTHER and Gene3D, have joined InterPro. A detailed description of the project can be found in the user manual.

This release marks the 5th anniversary of InterPro, a brief history of the database and the milestones in its development are outlined in "History and Development".

Changes since last release

Protein matches have been updated according to the latest update of UniProt and new methods from Gene3D, PANTHER, Pfam, PIRSF, PROSITE and TIGRFAMs, have been integrated.

InterPro entries have a new webpage design:

A new version of InterProScan is available; InterPro matches and matches to GO terms can be displayed and InterPro results can be filtered by taxonomy.

Contents and coverage of the current release

InterPro protein matches are now calculated for all UniProt proteins, which are a combination of UniProt/Swiss-Prot, UniProt/TrEMBL and PIR proteins. For more information see UniProt.

InterPro release 10.0 contains 11972 entries, representing 3079 domains, 8597 families, 228 repeats, 27 active sites, 21 binding sites and 20 post-translational modification sites. Overall, there are 7521179 InterPro hits from 1466570 UniProt protein sequences. A complete list is available from the ftp site.

DATABASE VERSION ENTRIES
SWISS-PROT 46.5 180652
PRINTS 37.0 1850
TrEMBL 29.5 1689375
Pfam 17.0 7868
PROSITE patterns 18.45 1800
PROSITE preprofiles N/A 120
ProDom 2004.1 1522
InterPro 10.0 11972
SMART 4.0 663
TIGRFAMs 4.1 2454
PIRSF 2.52 962
PANTHER 5.0 438
SUPERFAMILY 1.65 1160
Gene3D 3.0 117
GO Classification N/A 18705

91.8% of UniProt/Swiss-Prot - 165778 of 180652 proteins

77.0% of UniProt/TrEMBL - 1300792 of 1689375 proteins

78.4% of UniProt - 1466570 of 1870027 proteins

Last entry: IPR012680

19604 publications in PUBMED are referenced from InterPro.

Forthcoming changes

The next release of InterPro will be release 10.1 scheduled for July 2005. It will incorporate: